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Analysis of Genomic Aberrations and Gene Expression Profiling Identifies Citation: Blood Cancer Journal (2011) 1, e40; doi:10.1038/bcj.2011.39 & 2011 Macmillan Publishers Limited All rights reserved 2044-5385/11 www.nature.com/bcj ORIGINAL ARTICLE Analysis of genomic aberrations and gene expression profiling identifies novel lesions and pathways in myeloproliferative neoplasms KL Rice1, X Lin1, K Wolniak1, BL Ebert2, W Berkofsky-Fessler3, M Buzzai4, Y Sun5,CXi5, P Elkin5, R Levine6, T Golub7, DG Gilliland8, JD Crispino1, JD Licht1 and W Zhang5 1Division of Hematology/Oncology, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA; 2Division of Hematology, Department of Medicine, Brigham and Women’s Hospital, Boston, MA, USA; 3Translational Research Sciences, Hoffmann-La Roche, Inc., Nutley, NJ, USA; 4Oncology, Novartis, Origgio, VA, Italy; 5Division of Hematology/ Oncology, Department of Medicine, Center of Biomedical Informatics, Mount Sinai School of Medicine, New York, NY, USA; 6Human Oncology and Pathogenesis Program and Leukemia Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA; 7The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA and 8Oncology, Merck Research Laboratories, North Wales, PA, USA Polycythemia vera (PV), essential thrombocythemia and by a recurrent mutation, JAK2V617F, which is present in B95% primary myelofibrosis, are myeloproliferative neoplasms of patients with PV, B65% with PMF and B55% with ET.2 JAK2 (MPNs) with distinct clinical features and are associated with is one member of the Janus family of non-receptor tyrosine the JAK2V617F mutation. To identify genomic anomalies involved in the pathogenesis of these disorders, we profiled kinases that transduces signals downstream of type I and II 87 MPN patients using Affymetrix 250K single-nucleotide cytokine receptors via signal transducer and activators of polymorphism (SNP) arrays. Aberrations affecting chr9 were transcription (STATs), and is an important regulator of cell the most frequently observed and included 9pLOH (n ¼ 16), survival, proliferation, differentiation and apoptosis.3,4 The trisomy 9 (n ¼ 6) and amplifications of 9p13.3–23.3 (n ¼ 1), JAK2V617F mutation leads to autophosphorylation of JAK2 9q33.1–34.13 (n ¼ 1) and 9q34.13 (n ¼ 6). Patients with trisomy and constitutive activation of downstream pathways including 9 were associated with elevated JAK2V617F mutant allele burden, suggesting that gain of chr9 represents an alternative the Janus kinase (JAK)/STAT, phosphatidylinositol 3 kinase/AKT mechanism for increasing JAK2V617F dosage. Gene expres- (v-akt murine thymoma viral oncogene homolog 1) and sion profiling of patients with and without chr9 abnormalities mitogen-activated protein kinase (MAPK)/extracellular signal- ( þ 9, 9pLOH), identified genes potentially involved in disease regulated kinase pathways.5–9 Although overexpression of pathogenesis including JAK2, STAT5B and MAPK14. We also JAK2V617F in a murine bone marrow transplant models leads observed recurrent gains of 1p36.31–36.33 (n ¼ 6), 17q21.2– to a PV-like disease and megakaryocytic hyperplasia, such mice q21.31 (n ¼ 5) and 17q25.1–25.3 (n ¼ 5) and deletions affecting 18p11.31–11.32 (n ¼ 8). Combined SNP and gene expression do not develop thrombocytosis and questions regarding the analysis identified aberrations affecting components of a non- effect of allele dosage on disease phenotype remain unan- canonical PRC2 complex (EZH1, SUZ12 and JARID2) and genes swered. The finding of Theocharides et al.10 that 70% of comprising a ‘HSC signature’ (MLLT3, SMARCA2 and PBX1). JAK2V617F-positive MPN patients went on to develop We show that NFIB, which is amplified in 7/87 MPN patients and JAK2V617F-negative acute myeloid leukemia (AML), suggests upregulated in PV CD34 þ cells, protects cells from apoptosis that additional predisposing factors may precede the JAK2 induced by cytokine withdrawal. mutation. Recently, several acquired inactivating mutations in Blood Cancer Journal (2011) 1, e40; doi:10.1038/bcj.2011.39; 11 (ref. 12) (ref. 13) published online 11 November 2011 TET2, ASXL1 and IDH1/2 in MPN progenitors Keywords: myeloproliferative neoplasms; JAK2V617F; NFIB; SNP were identified, and it is likely that additional genes are involved in the initiation of a pre-leukemic clone or as disease modifiers, in co-operation with JAK2V617F. Previous studies using standard karyotyping revealed abnorm- Introduction alities in 50% of PMF patients, 15% of PV and o5% of ET patients.14–16 Although such conventional chromosome analysis The Ph-negative myeloproliferative neoplasms (MPNs) including has proven useful for diagnosis and prognostic information in polycythemia vera (PV), essential thrombocythemia (ET) and PMF patients and other myeloid malignancies, the sensitivity of primary myelofibrosis (PMF) are clonal hematopoietic disorders these approaches is limited. Indeed, studies by Tefferi using characterized by the overproduction of blood cells belonging to comparative genomic hybridization (CGH) oligonucleotide the myeloid, megakaryocytic and/or erythroid lineages.1 arrays to identify genomic aberrations in a panel of MPN Although clinically distinct, these diseases are characterized patients, detected copy number aberrations (CNAs) in 29% and 18% of patients with PV and ET, respectively, while cytoge- netics for these patients appeared normal.17 Recently, high- Correspondence: Dr W Zhang, Division of Hematology/Oncology, Department of Medicine, Center of Biomedical Informatics of Mount resolution single-nucleotide polymorphism (SNP) arrays have Sinai School of Medicine, Mount Sinai School of Medicine, One emerged as a powerful, high-throughput technology to allow Gustave L Levy Place, New York, NY 10029, USA. detection of micro-deletions and duplications and inference of E-mail: [email protected] loss of heterozygosity (LOH) from genotype calls, in cases where or Professor JD Licht, Division of Hematology/Oncology, Department conventional cytogenetic technologies and array CGH are of Medicine, Robert H Lurie Comprehensive Cancer Center, unsuccessful. Since then, SNP arrays have been successfully Northwestern University Feinberg School of Medicine, 303 East Superior Street, Lurie 5-123, Chicago, IL 60611, USA. used to identify cryptic oncogenic deletions and duplications E-mail: [email protected] affecting putative oncogenes and tumor suppressors in various Received 16 June 2011; accepted 11 August 2011 hematological malignancies. For example, the identification of Identification of novel lesions and pathways in MPN KL Rice et al 2 abnormalities on chromosome 4q24 affecting the TET2 gene in then used to determine the JAK2V617F allele burden (%) in patients with MDS, MPN and AML was facilitated by use of SNP DNA extracted from individual patient granulocytes. array analysis.11,18 Similarly, PAX5 was identified as a target for mutation in B-cell acute lymphocytic leukemia using SNP arrays.19 Recent studies using high-resolution SNP arrays Data analysis identified novel, recurrent aberrations in a large cohort of CNA analysis. These data were processed and analyzed MPN patients and revealed associations between specific using a custom developed procedure (Supplementary Figure S1). chromosomal anomalies and disease progression.20 Genotype calls were generated by GTYPE (Affymetrix) from CEL Here, we report an integrative analysis of chromosomal files and 250K library files for Nsp arrays. Raw data were abnormalities and gene expression changes in MPN patients. normalized using invariant set normalization method. The We profiled CNAs in peripheral blood granulocytes of 87 intensity value for each SNP was extracted using a model-based patients with MPN and identify new regions affected by perfect match/mismatch algorithm in dChip (http://biosun1. recurrent chromosomal aberrations. In a subset of the profiled harvard.edu/complab/dchip/). The log2 ratio of the intensity patients, genomic copy number changes could be correlated for each SNP for each sample relative to data from 60 with gene expression in granulocytes, leading to the identifica- unrelated CEU subjects of HapMap project (http://www. tion of novel genes deregulated in MPN. We show that patients hapmap.org) was calculated. The circular binary segment affected by chromosome 9 abnormalities, which represent the algorithm implemented in BioConductor DNAcopy package most frequent CNA, are characterized by deregulation of set of (http://bioconductor.org) was applied to the log2 ratio data to genes including JAK2, STAT5B and MAPK14, suggesting that segment the chromosome into contiguous regions of equal copy these genes may be involved in disease pathogenesis. We also number based on a maximal t-statistics with the use of a performed meta-analysis of five independent MPN expression permutation reference distribution (using coordinates of the SNP data sets to identify genes commonly deregulated in MPN. based on Genome Build HG-17).22 Segmental value was Comparison of genes identified in these meta-analysis with calculated by averaging copy number change values for the those affected by CNAs, revealed genes that may have important SNPs residing in that segment. The baseline value of genome- roles in disease pathogenesis including EZH1, MLLT3, SOCS3 wide segments in the sample with a bias in regional changes (in and SMARCA2. Finally, we show that the transcription factor case of the samples with more regional gains than losses, or vice NFIB, which is located adjacent
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